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The file can be mounted manually via 'cryptsetup luksOpen' and 'mount /dev/mapper' but I would like it to be mounted automatically while logging in and by showing a GUI dialog for the passphrase just like gnome/nautilus/ubuntu (?) is doing when an encrypted mass storage USB device is connected.

The (loopback) file containing the encrypted file system, is stored in a user's non-encrypted home directory.

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Gnome has a 'startup applications' program. If you are using Unity you should just be able to access it with <Super> start <ENTER>. From here enter the command that makes the prompt pop up. Unfortunately I wasn't quite sure what you are referring to, so I can't tell you how to do that. Another method is contained on the ubuntu wiki for FolderEncryption

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The GUI dialog looks like this: link It is automatically displayed when a LUKS encrypted USB mass storage device is connected, but I don't know how. Based on some googling I suspect that Nautilus is involved somehow. – Ulrik Feb 12 '13 at 20:32

if you have cryptsetup, configure your /etc/crypttab:

#<target name><source device><key file><options>
dm-2    UUID=XXXX  arg  luks,keyscript=/root/,noearly

cryptsetup will execute /root/ arg and all it gives on output takes as passphrase to unlock devices.

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